Questions tagged [proteins]
Questions relating to proteins, the chains of amino acids that form three-dimensional structures carrying important functions of life. Protein sequence, structure, similarity, domains, etc.
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How many protein sequences do we usually have for each species?
My question is exactly the one in the title. I add a particular example for more clarity. If I want to study the sequence of protein IkBα, do I find only one sequence or is there a database that ...
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plot the relation between RMSD and free energy
how can i plot the relation between rmsd and free energy like the image i attached as i need to find the most stable conformation structure for my cycle peptide after finishing REMD simulation
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Creating a scatterplot by a json data in js
I have a json file of protein data of mouse and human like
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How to get the nucleotide sequence for protein NCBI accession code, programatically?
It is a lot easier in my work to do blast searches against protein databases when I can, since I work with distantly related organisms. But sometimes, I need to work with the actual nucleotide ...
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Running into an error when loading Flexaid on PyMol 3.7
I have attached a screenshot from terminal, which is the result of me attempting to run Flexaid on my Mac.
I was wondering if anyone knows why this isn't running?
Thanks
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How to find/build the evolutionary history of a protein from its sequence?
I'd like to build the evolutionary history of a protein, given its sequence. Namely, given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein as an example:
...
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How to calculate RMSD and binding energy from the already docked ligand-receptor
I have the following PDB file that looks like this.
It is downloadable here. This PDB already contains ligand and receptor together.
The red molecule is the ligand and the yellow is the receptor.
They'...
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Align the HIV-1 Gag protein with the Gag protein of Visna virus
Align the HIV-1 Gag protein with the Gag protein of Visna virus
Background Visna virus is a lentivirus causing encephalitis in sheep
The problem is align the follow two protein Gag of viruses HIV-1 (...
M__♦
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finding motifs in fasta file with multiple sequences
I am able to find matching motifs on a single sequence, as well as their position as shown below :
...
CommunityBot
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What is protein secondary structure assignment?
I am absolutely new to Structural Bioinformatics (I only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using ML.
When it comes ...
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Histogram plot using R/python with two variables[BC and Control] and their corresponding gene names
How do we plot histogram in R\Python with two variables[BC and Control] and their corresponding gene names examples is below:
Thank you,
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Molecular dynamic simulation, reconstuction of protonation pattern of a protein from PDB file without resolvent hydrogen
I'm trying to build a topology of a protein using GROMACS. The pdb file do not include coordinates of hydrogen atoms. So I was wondering how to assign appropriate protonation states for each residue. ...
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Retrieval protein definition from accession ID
I have a list of protein accessions:
XP_025107904.1
PVD22034.1
AJA37836.1
How can I obtain the definition of the protein, and the related organism?
Output:
...
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How to retrieve sequences from a txt file by protein names from other txt file?
My problem is that I want to retrieve the sequences line + secondary structure line that match the protein names from the header.txt file:
The text file(...
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To find amino acid substitution from fasta alignment
I have fasta multiple sequence alignment file of protein sequence. I want to look for mutation/substitution in amino acid between query with reference to one query. Is there any R package or any ...
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Automating download of results of Drug and Drug Target Mapping
The drug and drug target mapping tool shows the top 3 PDB IDs for each drug based on the drug target sequence similarity search and ligand id search. Is there a way to get all the PDB ids of the drug-...
CommunityBot
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open and read Fasta file (raw data)
I have a big fasta.dataset file containing half a million proteins (1.0 GB). I have four lines for each protein code:
line 1:the protein code
line 2: protein ...
M__♦
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On the same strand, for the same gene, can exons be overlapping?
I want to get a set of exon regions for each protein coding gene.
I extracted a set of relevant information (chromosome, start, end, gene ID, gene name, gene type, exon number and exon ID) from a GTF ...
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How to calculate average BLOSUM62 scores?
I can understand the motive behind the BLOSUM62 matrix, this being a pairwise mutation matrix describing aggregate mutations between the 20 amino acids.
However how would you calculate the average ...
CommunityBot
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Heat map of protein expression from normalized abundance
This is a follow up to my question posted here
Processing proteomics data
In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article ...
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expansions and contractions from OrthoFinder
The input file looks like this, and the complete file can be found here:
...
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Help using BioPython's IC_Chain functionality for getting protein 3D coordinates from torsion angles
I have been successfully using BioPython's functionality for extracting protein torsion angles using the IC_Chain module. However, I am currently looking to use the ...
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What is changed in this PDB file?
I used a tool called reduce to add Hydrogen bonds information to the PDB file.
I used the command:
$ ./reduce -NOFLIP 2GB1.pdb > 2GB1_with_H.pdb
The output file ...
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Searching motifs in sequence and their frequencies
This is a two part question.
I am searching for a motif, and in that search I wanted to also find the total number of sequences in my FASTA file, but the code I wrote is not yielding that please see ...
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How can I get the coordinates of Hydrogen atoms attached to alpha-carbon?
I am trying to extract the hydrogen atoms attached to the Ca carbon in N no. of proteins. I would be needing the coordinates to calculate its centroid. How should I do it in python ?
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amino acids substitution probability
I am performing amino acid analysis but require assistance in the underlying amino acid substitution model, i.e. the predetermined rate/frequency of amino acid mutations which are used for example in ...
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What is the function of the heteroatoms
I am trying to make a prediction application using the sequence of proteins.
If we think about the 6COU protein, I'm running the code below
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Why does this modification site file contain duplicate sites and multiple related proteins?
The data below is coming from a MaxQuant post-translational protein modification (PTM) site file.
Why does it contain duplicate sites (yellow) and proteins (cyan)?
Source data
http://ftp.ebi.ac.uk/...
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How can I remove FASTA sequences with an asterisk inside the sequence?
I have several protein sequences with an asterisk in the middle of the sequence, and I'd like to remove those sequences.
In the example below, I have three sequences:
From this example, I would like ...
M__♦
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Why am I not being able to detect all the bonds in a residue?
Let us consider the first seven atoms of the protein 1CRN.pdb:
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Can the information regarding atomic bonds be interpreted only from atom lines in a PDB file?
The following are the first 14 atoms from the protein 1CRN:
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How can I extract the Protein distance map data in Julia?
I calculated the distance between C-alphas using Julia,
but there is no way to extract distance map data from Julia.
I don't even know the data file form, png or csv or etc.
I don't want to extract it ...
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finding the frequency of a motif-matching peptide
This question has also been asked on Biostars
I want to find the frequency of each motif-matching peptide.
The sequences are:
...
M__♦
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Why do we need to find minimum energy in a protein chain?
High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models
The above research paper is about a software tool for reconstructing a protein's main chain model only ...
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What is the difference between profile and pattern in Prosite?
I found a definition:
"A pattern is thus a qualitative description of a motif in terms of amino acid sequence. The concept of a profile extends this concept, allowing a quantitative description ...
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finding overlapping motifs to increase length of motif
I am able to find matching motif in my sequence, and I would like to now find overlapping motifs. Basically, after matching my motif, I want to find the 6 amino acids after it. This is the code below ...
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motif searching in a multi-fasta file
I am having trouble trying to search for motifs in a multi fasta file. I have used two techniques one gives me the name of the sequence where the motif is found but doesn't give me the the motif and ...
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Non-parametric, background-based tests on proteomics data from Proteome Discoverer v2.5?
I am new to proteomics analysis, so apologies if my question is silly! For context, I am working with proteome samples from the postmortem human brain for a case-control study.
Our lab generally ...
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What are all the proteins used to train Alphafold 2?
I want to identify the proteins used on AlphaFold2. The website says it was trained on PDB files from before April 30th 2018, and templates that are used are from no later than Feb 15 2021 (although ...
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PyMol alignment script
Is there a way write a script in python to use "super" to align proteins from a 2D array? Each row of the array has 2 columns, and for each row, I want to "super" the two proteins (...
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Select representetive sequence within MSA (protein)
I am trying to pick the best representative sequence from an amino acid MSA. I do not want to use the consensus, as it generates an artificial one. Here is my approach:
I calculate a Percentage ...
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Relationship between entries for same UniProt Id
I was playing around, looking at some AlphaFold predictions for certain proteins and I realized that sometimes the sequences of aminoacid look very different for the same UniProt id. For example, 15C8 ...
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How do I read mmCIF files from Alphafold DB as coordinates to use in replicating their visualization for Unity VR?
https://alphafold.com/entry/Q9Y499
Starting at line 918 of the downloadable mmCIF file, it looks like there might be coordinates in x, y,z:
...
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Permutations of 4 amino acid sequence oligopeptide
I have an assignment for a project to build a tetrapeptides library to screen against some target enzymes in silicon.
I am looking for a script to construct about 160000 tetrapeptide from the 20Amino ...
M__♦
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Python script to calculate properties of amino acids and storing them in matrix
I want to make a python script that can get as input sequence of N amino acids, and the output is a matrix of Nx6 containing 6 features.
The features are:
Computed volume
Hydrophobicity
Surface ...
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mass spectrum matching with cyclic peptide and linear peptide
I was doing a simple quiz which I encountered the following two questions related to mass spectrum matching with cyclic peptide and linear peptide.
I have done some preliminary google search, but I am ...
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Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions
I'm trying to programmatically replace a set of amino acid residues on an MSA with a "Z" from a list of unaligned positions. Any ideas on how I could do this?
Input: a list of unaligned ...
M__♦
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Convert .smp downloaded from NCBI CDD into HMM(.hmm) file [closed]
Is there a method or tool to convert a .smp file from CDD (Protein Domain File) into a HMM file? I downloaded the CDD files from the FTP site and am more familiar with domain searching with the HMMer ...
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Multifasta protein alignment
I have around 4000 orthologous proteins for each of 5 species, I'd like to align them and to concatenate alignments. Which tools can I use? And how?
Marco
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How can I parse alternative atom information?
I am trying to parse PDB files.
Say, a PDB file has the following data:
...
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